Changed ***key-certbot.pem file caused server offline - lets-encrypt

Question

Server: Nginx on Ubuntu 16.04 Xenial
Our sites "crashed" just now due to a certificate issue:
nginx: [emerg] SSL_CTX_use_PrivateKey_file("/etc/letsencrypt/keys/0000_key-certbot.pem") failed (SSL: error:0B080074:x509 certificate routines:X509_check_private_key:key values mismatch)
nginx: configuration file /etc/nginx/nginx.conf test failed
In the Virtual hosts, we have these lines:
ssl_certificate_key /etc/letsencrypt/keys/0003_key-certbot.pem;
ssl_certificate /etc/letsencrypt/live/[domain]/fullchain.pem;
On checking the /etc/letsencrypt/keys/ folder, I found these results
/etc/letsencrypt/keys # ls -la
total 40
drwx------ 2 root root 4096 Jul 5 15:33 .
drwxr-xr-x 11 root root 4096 Apr 18 10:58 ..
-rw------- 1 root root 1704 Apr 18 11:01 0000_key-certbot.pem
-rw------- 1 root root 1708 Jan 31 14:37 0000_key-letsencrypt.pem
-rw------- 1 root root 1704 Apr 18 11:18 0001_key-certbot.pem
-rw------- 1 root root 1704 Jan 31 14:37 0001_key-letsencrypt.pem
-rw------- 1 root root 1704 Apr 18 11:19 0002_key-certbot.pem
-rw------- 1 root root 1708 Feb 2 11:47 0002_key-letsencrypt.pem
-rw------- 1 root root 1708 Jun 17 12:01 0003_key-certbot.pem
-rw------- 1 root root 1704 Jul 5 15:33 0004_key-certbot.pem
The (3) virtual host files were all referencing 0000_key-certbot.pem, after changing that to 0003_key-certbot.pem the sites were working again.
How can we prevent the sites from crashing every 90 days?

Answer 1

While typing this I think I found the solution, I shouldn't have been using
ssl_certificate_key /etc/letsencrypt/keys/0003_key-certbot.pem;
ssl_certificate /etc/letsencrypt/live/[domain]/fullchain.pem;
But instead
ssl_certificate_key /etc/letsencrypt/live/[domain]/privkey.pem;
ssl_certificate /etc/letsencrypt/live/[domain]/fullchain.pem;
Hope this helps someone